User: Chironex

gravatar for Chironex
Chironex30
Reputation:
30
Status:
New User
Location:
rome
Last seen:
1 year, 4 months ago
Joined:
2 years, 1 month ago
Email:
o************@gmail.com

Posts by Chironex

<prev • 45 results • page 1 of 5 • next >
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correlation between element-gene
... I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element in samples: M1 <- elements ova testes re ...
R correlation written 17 months ago by Chironex30
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tool to detect the role of transposon on genic regulation
... Hello everyone, I'm looking for an advice. I found some transposable elements with repeatmaskers in an assembled genome. what interests me now is to check the position of some transposons in different genes to try to understand their role on gene expression. could you recommend a program in R that i ...
R transposon written 20 months ago by Chironex30
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Comment: C: normalization with RPKM
... Stringtie is not implemented in R, right? ...
written 21 months ago by Chironex30
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Comment: C: normalization with RPKM
... Is it usable even if elements are not genes, but transposon? the gtf file of featurecounts is the output of repeatmasker analysis ...
written 21 months ago by Chironex30
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normalization with RPKM
... hello! I'm very i difficult with normalization of my data. I was searching for transposable elements in my genome, and after this step, I made counts of reads in some transcripts. I produced something like that: head(table_tissues_filtered_TE) Lengths ova testes lobe retin ...
normalization transposon data rna-seq rpkm written 21 months ago by Chironex30 • updated 14 months ago by Biostar ♦♦ 20
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Comment: C: repeatmasker species setting
... ~/RM/RepeatMasker/util$ ls -l totale 204 -rwxr-xr-x 1 fragua fragua 4622 nov 21 2018 buildRMLibFromEMBL.pl -rwxr-xr-x 1 fragua fragua 22868 nov 21 2018 buildSummary.pl -rwxr-xr-x 1 fragua fragua 10430 nov 21 2018 calcDivergenceFromAlign.pl -rwxr-xr-x 1 fragua fragua 20607 ...
written 21 months ago by Chironex30
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Comment: C: repeatmasker species setting
... If I put `~/RM/RepeatMasker/util$ queryRepeatDatabase.pl -h` , it says to me queryRepeatDatabase.pl: command not found ...
written 21 months ago by Chironex30
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Comment: C: repeatmasker species setting
... okay, thank you for your help! ...
written 21 months ago by Chironex30
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Comment: C: repeatmasker species setting
... okay, but repeatmasker will be able to recognize the library created by myself finding transposable elements? I've tried using Repeatscout, but the results didn't are the expected. Repeatmodeler is different? ...
written 21 months ago by Chironex30
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repeatmasker species setting
... hello! I'm working with a genome of cephalopoda. Firstly, I ran Repeatmasker with this input /home/RM/RepeatMasker -s -gff OB150DEC_2.fa to analyze the genome assuming that the specie is homo sapiens. I'm not sure that it is correct, because I suppose that transposable elements could be dif ...
genome repeatmasker written 21 months ago by Chironex30 • updated 21 months ago by Juke345.2k

Latest awards to Chironex

Scholar 20 months ago, created an answer that has been accepted. For C: error RepeatMasker Installation

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